Lanthanide spectroscopic studies of the dinuclear and Mg(II)-dependent PvuII restriction endonuclease

Biochemistry

Volumn 43, Issue 48, 2004, Pages 15286-15292

  Bowen, Lori M ^a   Muller, Gilles ^b,c   Riehl, James P ^b   Dupureur, Cynthia M ^a  

^a UNIVERSITY OF MISSOURI ST LOUIS   (United States)

^b UNIVERSITY OF MINNESOTA DULUTH   (United States)

^c SAN JOSE STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; DIMERS; DNA SEQUENCES; ESTERS; LUMINESCENCE; MATHEMATICAL MODELS; RARE EARTH ELEMENTS; SPECTROSCOPIC ANALYSIS;

BINDING SITES; ENZYME STRUCTURE; LANTHANIDE SPECTROSCOPY; LUMINESCENCE SPECTROSCOPY;

ENZYMES;

CALCIUM; EUROPIUM; LANTHANIDE; MAGNESIUM DERIVATIVE; MANGANESE; TERBIUM; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; TYROSINE;

ARTICLE; BINDING AFFINITY; DNA BINDING; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME MECHANISM; ENZYME SUBSTRATE; LUMINESCENCE; METAL BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; SPECTROSCOPY;

BINDING SITES; BINDING, COMPETITIVE; BUFFERS; CATIONS, DIVALENT; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA-BINDING PROTEINS; EUROPIUM; LANTHANOID SERIES ELEMENTS; LUMINESCENT MEASUREMENTS; MAGNESIUM; MAGNETIC RESONANCE SPECTROSCOPY; PROTEUS VULGARIS; SPECTROMETRY, FLUORESCENCE; TERBIUM; TYROSINE;

EID: 10044251064     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0486278     Document Type: Article

References (50)

1. Cowan, J. A. (1997) Inorganic Biochemistry, an Introduction, Wiley-VCH, New York.
2. Beese, L. S., and Steitz, T. A. (1991) Structural basis for the 3′-5′ exonuclease activity of Escherichia coli polymerase I: A two metal ion mechanism, EMBO J. 10, 25-33.
3. Suck, D., Oefner, C., and Kabsch, W. (1984) Three-dimensional structure of bovine pancreatic DNase I at 2.5 Å resolution, EMBO J. 3, 2423-2430.
4. DeRose, V. (2003) Metal ion binding to catalytic RNA molecules, Curr. Opin. Struct. Biol. 13, 317-324.
5. Pingoud, A., and Jeltsch, A. (2001) Structure and function of type II restriction endonucleases, Nucleic Acids Res. 29, 3705-3727.
6. Gormley, N. A., Bath, A. J., and Halford, S. E. (2000) Reactions of BglI and other type II restriction endonucleases with discontinuous recognition sites, J. Biol. Chem. 275, 6928-6936.
7. Bowen, L. M., and Dupureur, C. M. (2003) Investigation of restriction enzyme cofactor requirements: A relationship between metal ion properties and sequence specificity, Biochemistry 42, 12643-12653.
8. Vipond, I. B., and Halford, S. E. (1995) Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions, Biochemistry 34, 1113-1119.
9. Lagunavicius, A., Grazulis, S., Balciunaite, E., Vainius, D., and Siksnys, V. (1997) DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: Involvement of active site carboxylate residues, Biochemistry 36, 11093-11099.
10. Conlan, L. H., and Dupureur, C. M. (2002) Dissecting the metal ion dependence of DNA binding by PvuII endonuclease, Biochemistry 41, 1335-1342.
11. José, T. J., Conlan, L. H., and Dupureur, C. M. (1999) Quantitative evaluation of metal ion binding to PvuII restriction endonuclease, J. Biol. Inorg. Chem. 4, 814-823.
12. Dupureur, C. M., and Conlan, L. H. (2000) A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions, Biochemistry 39, 10921-10927.
13. Martin, R. B. (1984) in Metal Ions in Biological Systems (Sigel, H., Ed.) Vol. 17, pp 32-49, Marcel Dekker, New York.
14. Moeller, T. (1963) The Chemistry of the Lanthanides, Reinhold, New York.
15. Martell, A. E., and Smith, R. M. (1989) Critical Stability Constants, Plenum, New York.
16. Bruno, J., Horrocks, W. D., Jr., and Zauhar, R. J. (1992) Europium(III) luminescence and tyrosine to terbium(III) energy-transfer studies of invertebrate (octopus) calmodulin, Biochemistry 31, 7016-7026.
17. 0 spectrum. FEBS Lett. 314, 130-134.
18. Walters, J. D., and Johnson, J. D. (1990) Terbium as a luminescent probe of metal-binding sites in protein kinase C, J. Biol. Chem. 265, 4223-4226.
19. Frey, M. W., Frey, S. T., Horrocks, W. D., Jr., Kaboord, B. F., and Benkovic, S. J. (1996) Elucidation of the metal-binding properties of the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase by lanthanide(III) luminescence spectroscopy, Chem. Biol. 3, 393-403.
20. Lin, W., Dombrosky, P., Atkins, W., and Villafranca, J. (1991) Terbium(III) luminescence study of tyrosine emission from Escherichia coli glutamine synthetase, Biochemistry 30, 3427-3431.
21. Feig, A., Panek, M., Horrocks, W. D., Jr., and Uhlenbeck, O. (1999) Probing the binding of Tb(III) and Eu(III) to the hammerhead ribozyme using luminescence spectroscopy, Chem. Biol. 6, 801-810.
22. Horrocks, W. D., Jr. (1982) Lanthanide probes of biomolecular structure, Adv. Inorg. Chem. 4, 201-261.
23. Horrocks, W. D. (1993) Luminescence spectroscopy, Methods Enzymol. 226, 495-538.
24. Holmquist, B. (1988) Elimination of Adventitious Metals, Methods Enzymol. 158, 6-12.
25. Dupureur, C. M., and Hallman, L. M. (1999) Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases, Eur. J. Biochem. 261, 261-268.
26. Wagner, F. W. (1988) Preparation of metal-free enzymes, Methods Eniymol. 158, 21-32.
27. Muller, G., Kean, S. D., Parker, D., and Riehl, J. P. (2002) Temperature and pressure dependence of excitation spectra as a probe of the solution structure and equilibrium thermodynamics of a Eu(III) complex containing a modified dota ligand, J. Phys. Chem. A 106, 12349-12355.
28. ITC Data Analysis in Origin (1993), Microcal, Inc., Northampton, MD.
29. Martin, R. B., and Richardson, F. S. (1979) Lanthanides as probes for calcium in biological systems, Q. Rev. Biophys. 12, 181-209.
30. Brittain, H. G., Richardson, F. S., and Martin, R. B. (1976) Terbium(III) emission as a probe of calcium(II) binding sites in proteins, J. Am. Chem. Soc. 98, 8255-8260.
31. 2+ binding site near Tyr94 in the restriction enzyme PvuII, J. Mol. Biol 331, 395-406.
32. Horton, J. R., and Cheng, X. (2000) PvuII endonuclease contains two calcium ions in active sites, J. Mol. Biol. 300, 1049-1056.
33. Luk, C. K. (1971) Study of the nature of the metal-binding sites and estimate of the distance between the metal-binding sites in transferrin using trivalent lanthanide ions as fluorescent probes, Biochemistry 10, 2838-2843.
34. Wallace, R. W., Tallant, E. A., Dockter, M. E., and Cheung, W. Y. (1982) Calcium binding domains of calmodulin, J. Biol. Chem. 257, 1845-1854.
35. Shannon, R. D. (1976) Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides, Acta Crystallogr. A32, 751-767.
36. Matthews, B. W., and Weaver, L. H. (1974) Binding of lanthanide ions to thermolysin, Biochemistry 13, 1719-1725.
37. Chaudhuri, D., and Horrocks, W. D., Jr. (1997) Characterization of lanthanide ion binding to the EF-hand protein S100β by luminescence spectroscopy, Biochemistry 36, 9674-9680.
38. Reid, S. L., Parry, D., Liu, H.-H., and Connolly, B. A. (2001) Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarisation, Biochemistry 40, 2484-2494.
39. Conlan, L. H., and Dupureur, C. M. (2002) Multiple metal ions drive DNA association by PvuII endonuclease, Biochemistry 41, 14848-14855.
40. Nastri, H. G., Evans, P. D., Walker, I. H., and Riggs, P. D. (1997) Catalytic and DNA binding properties of PvuII restriction endonuclease mutants, J. Biol. Chem. 272, 25761-25767.
41. Cowan, J. A. (1995) The Biological Chemistry of Magnesium, VCH, New York.
42. Muller, G., Muller, F. C., and Riehl, J. P. (2004) On the use of high pressure to study the speciation, solvation, and excited-state energetics of luminescent lanthanide complexes, J. Alloys Compd., in press.
43. Riehl, J. P., and Muller, G. (2004) Review of Circularly Polarized Luminescence Spectroscopy from Lanthanide Systems, in Handbook on the Physics and Chemistry of Rare Earths (Gschneidner, K., Bunzli, J.-C. G., and Pecharksy, V. K., Eds.) Vol. 34, Chapter 220, in press, Holland Publishing Company, Amsterdam.
44. Greenbaum, N. L., Mundoma, C., and Peterman, D. R. (2001) Probing of metal-binding domains of RNA hairpin loops by laser-induced lanthanide(III) luminescence. Biochemistry 40, 1124-1134.
45. Waddington, T. (1959) Advances in Inorganic Chemistry and Radiochemistry, Vol. 1, Academic Press, New York.
46. Bruno, J., Horrocks, W. D., Jr., and Beckingham, K. (1996) Characterization of Eu(III) binding to a series of calmodulin binding site mutants using laser-induced Eu(III) luminescence spectroscopy, Biophys. Chem. 63, 1-16.
47. Black, C. B., and Cowan, J. A. (1998) A critical evaluation of metal-promoted Klenow 3′-5′ exonuclease activity: calorimetric and kinetic analyses support a one-metal-ion mechanism, J. Biol. Inorg. Chem. 3, 292-299.
48. Brautigam, C. A., Aschheim, K., and Steitz, T. A. (1999) Structural elucidation of the binding and inhibitory properties of lanthanide (III) at the 3′-5′ exonucleolytic active site of the Klenow fragment, Chem. Biol. 6, 901-908.
49. Kay, J., Moore, J. W., and Glick, M. (1972) Structural studies of bridged lanthanide(III) complexes. Diaquotri(nicotinic acid)-holmium hexa(isothiocynanato)chromate(III) dihydrate and diaquotris(isonicotinato) lanthanum(III), Inorg. Chem. 11, 2818-2827.
50. 4, J. Am. Chem. Soc. 94, 1858-1865.